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Related Concept Videos

General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying DNA...

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Related Experiment Video

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A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers
08:12

A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers

Published on: July 18, 2025

Predicting tissue-specific enhancers in the human genome.

Len A Pennacchio1, Gabriela G Loots, Marcelo A Nobrega

  • 1Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

Genome Research
|January 11, 2007
PubMed
Summary

Researchers identified thousands of novel tissue-specific enhancers in the human genome by integrating gene expression data and comparative genomics. This advance helps decode gene regulation and understand vertebrate complexity.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Understanding transcriptional regulatory signals in vertebrate genomes is crucial for deciphering multicellular complexity.
  • The genetic code governing vertebrate gene regulation is not yet fully understood.

Purpose of the Study:

  • To elucidate the genetic code of vertebrate gene regulation by identifying sequence signatures of tissue-specific enhancers.
  • To computationally predict and validate candidate enhancers across the human genome.

Main Methods:

  • Synergistic integration of genome-wide gene-expression profiling, vertebrate genome comparisons, and transcription factor binding-site analysis.
  • Application to microarray-based gene expression profiles from 79 human tissues to identify candidate enhancers.
  • Cross-validation using de novo prediction of tissue-specific gene expression and comparison with in vivo validated enhancers.

Main Results:

  • Identified 7187 candidate tissue-specific enhancers in the human genome, many located outside known promoters.
  • Achieved reliability in predicting tissue-specific gene expression across 57 of 79 human tissues, with 32-63% precision and 47% sensitivity.
  • Predicted tissue-specific regulatory roles for ~328,000 human-mouse conserved noncoding elements, validated with 50% precision and 28% sensitivity.

Conclusions:

  • Combining complementary genomic datasets is a powerful computational approach to globally map tissue-specific gene regulation in vertebrates.
  • This study provides significant insights into the sequence signatures and genomic locations of functional enhancers.
  • The findings contribute to a deeper understanding of the regulatory underpinnings of vertebrate evolution and complexity.